Chapter 10 Toward a Theory of Multilevel Evolution: Long-Term Information Integration Shapes the Mutational Landscape and Enhances Evolvability
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"Evolutionary Emergence of Genes Through Retrotransposition"
Evolutionary Emergence of Advanced article Genes Through Article Contents . Introduction Retrotransposition . Gene Alteration Following Retrotransposon Insertion . Retrotransposon Recruitment by Host Genome . Retrotransposon-mediated Gene Duplication Richard Cordaux, University of Poitiers, Poitiers, France . Conclusion Mark A Batzer, Department of Biological Sciences, Louisiana State University, Baton Rouge, doi: 10.1002/9780470015902.a0020783 Louisiana, USA Variation in the number of genes among species indicates that new genes are continuously generated over evolutionary times. Evidence is accumulating that transposable elements, including retrotransposons (which account for about 90% of all transposable elements inserted in primate genomes), are potent mediators of new gene origination. Retrotransposons have fostered genetic innovation during human and primate evolution through: (i) alteration of structure and/or expression of pre-existing genes following their insertion, (ii) recruitment (or domestication) of their coding sequence by the host genome and (iii) their ability to mediate gene duplication via ectopic recombination, sequence transduction and gene retrotransposition. Introduction genes, respectively, and de novo origination from previ- ously noncoding genomic sequence. Genome sequencing Variation in the number of genes among species indicates projects have also highlighted that new gene structures can that new genes are continuously generated over evolution- arise as a result of the activity of transposable elements ary times. Although the emergence of new genes and (TEs), which are mobile genetic units or ‘jumping genes’ functions is of central importance to the evolution of that have been bombarding the genomes of most species species, studies on the formation of genetic innovations during evolution. For example, there are over three million have only recently become possible. -
Experimental Evolution
Heredity (2008) 100, 441–442 & 2008 Nature Publishing Group All rights reserved 0018-067X/08 $30.00 www.nature.com/hdy EDITORIAL Experimental evolution Heredity (2008) 100, 441–442; doi:10.1038/hdy.2008.19 and their interactions, it should be possible to predict which genes will be altered, how they will be altered and in what order, in any defined environment. Our under- Microcosms are used in ecology and evolution to shrink standing of cell biology is as yet wholly inadequate for space and time to manageable scales. They have never the task, but the smaller genomes of viruses might be been extensively used in ecology, because many ecolo- more accessible. Bull and Molineux describe the most gists doubt that any important features of large complex ambitious attempts to date in pursuit of this grail, using systems, such as lakes, can be profitably investigated in phage T7 of E. coli. Given the detailed knowledge of T7 small chambers or vials (Carpenter, 1996). Consequently, genetics, it should be possible to introduce a specific ecology lacks any generally accepted model system genetic lesion and then predict what compensatory to facilitate the cumulative growth of understanding of mutations will be fixed so as to restore the lost function. how communities work. Evolutionary biologists have In many cases, these mutations were correctly identified been less skeptical, and at least three major schools and for very simple genomes, at least, a nearly complete have adopted microcosm methods. Perhaps the best understanding of adaptation seems to be within grasp. known is the extensive exploration of the effects of artificial selection in Drosophila (and to a lesser extent in At the same time, both Ferenci and Bull and Molineux other organisms, such as mice). -
Genome Organization/ Human
Genome Organization/ Secondary article Human Article Contents . Introduction David H Kass, Eastern Michigan University, Ypsilanti, Michigan, USA . Sequence Complexity Mark A Batzer, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA . Single-copy Sequences . Repetitive Sequences . The human nuclear genome is a highly complex arrangement of two sets of 23 Macrosatellites, Minisatellites and Microsatellites . chromosomes, or DNA molecules. There are various types of DNA sequences and Gene Families . chromosomal arrangements, including single-copy protein-encoding genes, repetitive Gene Superfamilies . sequences and spacer DNA. Transposable Elements . Pseudogenes . Mitochondrial Genome Introduction . Genome Evolution . Acknowledgements The human nuclear genome contains 3000 million base pairs (bp) of DNA, of which only an estimated 3% possess protein-encoding sequences. As shown in Figure 1, the DNA sequences of the eukaryotic genome can be classified sequences such as the ribosomal RNA genes. Repetitive into several types, including single-copy protein-encoding sequences with no known function include the various genes, DNA that is present in more than one copy highly repeated satellite families, and the dispersed, (repetitive sequences) and intergenic (spacer) DNA. The moderately repeated transposable element families. The most complex of these are the repetitive sequences, some of remainder of the genome consists of spacer DNA, which is which are functional and some of which are without simply a broad category of undefined DNA sequences. function. Functional repetitive sequences are classified into The human nuclear genome consists of 23 pairs of dispersed and/or tandemly repeated gene families that chromosomes, or 46 DNA molecules, of differing sizes either encode proteins (and may include noncoding (Table 1). -
Estimation of Duplication History Under a Stochastic Model for Tandem Repeats Farzad Farnoud1* , Moshe Schwartz2 and Jehoshua Bruck3
Farnoud et al. BMC Bioinformatics (2019) 20:64 https://doi.org/10.1186/s12859-019-2603-1 RESEARCH ARTICLE Open Access Estimation of duplication history under a stochastic model for tandem repeats Farzad Farnoud1* , Moshe Schwartz2 and Jehoshua Bruck3 Abstract Background: Tandem repeat sequences are common in the genomes of many organisms and are known to cause important phenomena such as gene silencing and rapid morphological changes. Due to the presence of multiple copies of the same pattern in tandem repeats and their high variability, they contain a wealth of information about the mutations that have led to their formation. The ability to extract this information can enhance our understanding of evolutionary mechanisms. Results: We present a stochastic model for the formation of tandem repeats via tandem duplication and substitution mutations. Based on the analysis of this model, we develop a method for estimating the relative mutation rates of duplications and substitutions, as well as the total number of mutations, in the history of a tandem repeat sequence. We validate our estimation method via Monte Carlo simulation and show that it outperforms the state-of-the-art algorithm for discovering the duplication history. We also apply our method to tandem repeat sequences in the human genome, where it demonstrates the different behaviors of micro- and mini-satellites and can be used to compare mutation rates across chromosomes. It is observed that chromosomes that exhibit the highest mutation activity in tandem repeat regions are the same as those thought to have the highest overall mutation rates. However, unlike previous works that rely on comparing human and chimpanzee genomes to measure mutation rates, the proposed method allows us to find chromosomes with the highest mutation activity based on a single genome, in essence by comparing (approximate) copies of the pattern in tandem repeats. -
Genomic Comparison of Closely Related Giant Viruses Supports an Accordion-Like Model of Evolution
ORIGINAL RESEARCH published: 16 June 2015 doi: 10.3389/fmicb.2015.00593 Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution Jonathan Filée * Laboratoire Evolution, Génome, Comportement, Ecologie, Centre National de la Recherche Scientifique UMR 9191, IRD UMR 247, Université Paris-Saclay, Gif-sur-Yvette, France Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the Edited by: different losses. In addition, each lineage displays specific patterns of genome evolution. Bernard La Scola, Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved Aix Marseille Université, France mainly by duplications and losses of genes belonging to large paralogous families Reviewed by: (including movements of diverse mobiles genetic elements), whereas Micromonas and Dahlene N. Fusco, Massachusetts General Hospital, USA Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral Philippe Colson, gene transfers. Taken together, these data support an accordion-like model of evolution Aix-Marseille Université, France in which GV genomes have undergone successive steps of gene gain and gene loss, *Correspondence: Jonathan Filée, accrediting the hypothesis that genome gigantism appears early, before the diversification Laboratoire Evolution, Génome, of the different GV lineages. -
Long-Term Experimental Evolution in Escherichia Coli. V. Effects of Recombination with Immigrant Genotypes on the Rate of Bacterial Evolution
© Birkhliuser Verlag, Basel, 1997 J. evol. bioi. 10 (1997) 743-769 1010-061X/97/050743-27 $ 1.50 + 0.20/0 I Journal of Evolutionary Biology Long-term experimental evolution in Escherichia coli. V. Effects of recombination with immigrant genotypes on the rate of bacterial evolution 1 2 3 V. Souza, P. E. Turner • and R. E. LenskF·* 1Centro de Ecologia, Universidad Nacional Aut6noma de Mexico, Coyoacim, Ciudad de Mexico, 04510, Mexico 2 Center for Microbial Ecology, Michigan State University, East Lansing MI 48824, USA 3 Current address: Department of Zoology, University of Maryland, College Park MD 20742, USA Key words: Complex selection; conjugation; Escherichia coli; experimental evolu tion; hitchhiking; migration; plasmids; recombination. Abstract This study builds upon an earlier experiment that examined the dynamics of mean fitness in evolving populations of Escherichia coli in which mutations were the sole source of genetic variation. During thousands of generations in a constant environment, the rate of improvement in mean fitness of these asexual populations slowed considerably from an initially rapid pace. In this study, we sought to determine whether sexual recombination with novel genotypes would reaccelerate the rate of adaption in these populations. To that end, treatment populations were propagated for an additional 1000 generations in the same environment as their ancestors, but they were periodically allowed to mate with an immigrant pool of genetically distinct Hfr (high frequency recombination) donors. These donors could transfer genes to the resident populations by conjugation, but the donors them selves could not grow in the experimental environment. Control populations were propagated under identical conditions, but in the absence of sexual recombination with the donors. -
Extrachromosomal Element Capture and the Evolution of Multiple Replication Origins in Archaeal Chromosomes
Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes Nicholas P. Robinson† and Stephen D. Bell† Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Center, Hills Road, Cambridge CB2 0XZ, United Kingdom Edited by Carl R. Woese, University of Illinois at Urbana–Champaign, Urbana, IL, and approved February 15, 2007 (received for review January 9, 2007) In all three domains of life, DNA replication begins at specialized Orc2–6 act to recruit MCM to origins of replication in a reaction loci termed replication origins. In bacteria, replication initiates from that absolutely requires an additional factor, Cdt1 (6). Although a single, clearly defined site. In contrast, eukaryotic organisms archaea possess orthologs of Orc1, Cdc6, and MCM, no archaeal exploit a multitude of replication origins, dividing their genomes homolog of Cdt1 has yet been identified. into an array of short contiguous units. Recently, the multiple In the current work, we reveal that Aeropyrum pernix has at replication origin paradigm has also been demonstrated within the least two replication origins, indicating that the multiple repli- archaeal domain of life, with the discovery that the hyperthermo- cation origin paradigm is not restricted to the Sulfolobus genus. philic archaeon Sulfolobus has three replication origins. However, Comparison of the A. pernix and Sulfolobus origins reveals a clear the evolutionary mechanism driving the progression from single to relationship between these loci. Further, analyses of the gene multiple origin usage remains unclear. Here, we demonstrate that order and identity in the environment of the origins provides Aeropyrum pernix, a distant relative of Sulfolobus, has two origins. -
Selection Experiments and Experimental Evolution of Performance and Physiology
Garland_ch12.qxd 8/3/09 2:03 PM Page 301 12 SELECTION EXPERIMENTS AND EXPERIMENTAL EVOLUTION OF PERFORMANCE AND PHYSIOLOGY John G. Swallow, Jack P. Hayes, Pawel Koteja, and Theodore Garland, Jr. THE IMPORTANCE OF REPLICATION Selection on VO2max and the Correlation between BMR and VO2max EXPERIMENTAL EVOLUTION OF MICE IN DIFFERENT THERMAL ENVIRONMENTS SEXUAL SELECTION: EFFECTS OF ORNAMENTS ON PERFORMANCE WIND TUNNEL FLIGHT IN DROSOPHILA Guppies ENDURANCE RUNNING AND STRESS-INDUCED ANALGESIA IN MICE Stalk-Eyed Flies ENDURANCE RUNNING IN RATS AND VOLUNTARY WHEEL “EXPERIMENTS” WITHOUT PRECISELY DEFINED SELECTION RUNNING IN MICE CRITERIA EVOLUTION OF THE RATE OF ENERGY METABOLISM Horse Racing IN RODENTS Greyhound Racing Selection on Basal Metabolic Rate PHYSIOLOGICAL DIFFERENCES AMONG STRAINS Selection on Heat Loss OF MICE AND BREEDS OF DOG Rate of Metabolism as a Hypothetical CONCLUSION Correlated Response Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments, edited by Theodore Garland, Jr., and Michael R. Rose. Copyright © by the Regents of the University of California. All rights of reproduction in any form reserved. 301 Garland_ch12.qxd 8/3/09 2:03 PM Page 302 Since a seminal paper by Arnold (1983), direct measurement of whole-organism perfor- mance has become central to functional evolutionary biology (e.g., Arnold 2003; Ghalambor et al. 2003; Kingsolver and Huey 2003). In this context, “performance” can be most easily defined by example. Assuming that individuals can be fully motivated (e.g., see Swallow et al. 1998a; Harris and Steudel 2002; Losos et al. 2002; Tobalske et al. 2004), it is relatively easy to measure maximal sprint running speed of small mammals and lizards on photocell-timed racetracks or high-speed treadmills (e.g., Calsbeek and Irschick 2007; Chappell et al. -
Mitochondrial DNA Duplication, Recombination, and Introgression During Interspecific Hybridization
www.nature.com/scientificreports OPEN Mitochondrial DNA duplication, recombination, and introgression during interspecifc hybridization Silvia Bágeľová Poláková1,5, Žaneta Lichtner1, Tomáš Szemes2,3,4, Martina Smolejová1 & Pavol Sulo1* mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfsh elements are benefcial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes. Hybrids between Saccharomyces species occur frequently in nature as a number of hybrids have been reported among wine and beer strains1–6. Most lager beer strains are hybrids between S. cerevisiae and S. eubayanus, combining the ability to produce ethanol with cryotolerance 6–8. Some S. cerevisiae × S. kudriavzevii strains are associated with beer, but most of them are associated with wine, where they provide unique favor8,9. S. eubayanus and S. uvarum hybrids have been associated with sparkling wine, cider fermentation, and, in some cases, with the production of of-favors in breweries 8,10,11. Interspecifc hybrids among Saccharomyces species can also be readily obtained in the laboratory 9,12–14. -
Darwinian Evolution in a Translation-Coupled RNA Replication System Within a Cell-Like Compartment
ARTICLE Received 28 Mar 2013 | Accepted 22 Aug 2013 | Published 3 Oct 2013 DOI: 10.1038/ncomms3494 Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment Norikazu Ichihashi1,2, Kimihito Usui1, Yasuaki Kazuta1, Takeshi Sunami1,2, Tomoaki Matsuura1,2,3 & Tetsuya Yomo1,2,4 The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators. 1 Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan. 2 Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan. 3 Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. 4 Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan. Correspondence and requests for materials should be addressed to T.Y. -
CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research CAGGG Repeats and the Pericentromeric Duplication of the Hominoid Genome Evan E. Eichler,1,3 Nicoletta Archidiacono,2 and Mariano Rocchi2 1Department of Genetics and Center for Human Genetics, Case Western Reserve School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106 USA; 2Instituto di Genetica, Via Amendola 165/A, 70126 Bari, Italy Gene duplication is one of the primary forces of evolutionary change. We present data from three different pericentromeric regions of human chromosomes, which indicate that such regions of the genome have been sites of recent genomic duplication. This form of duplication has involved the evolutionary movement of segments of genomic material, including both intronic and exonic sequence, from diverse regions of the genome toward the pericentromeric regions. Sequence analyses of the target sites of duplication have identified a novel class of interspersed GC-rich repeats located precisely at the boundaries of duplication. Estimates of the evolutionary age of these duplications indicate that they have occurred between 10 and 25 mya. In contrast, comparative analyses confirm that the GC-rich pericentromeric repeats have existed within the pericentromeric regions of primate chromosomes before the divergence of the cercopithecoid and hominoid lineages (∼30 mya). These data provide molecular evidence for considerable interchromosomal duplication of genic segments during the evolution of the hominoid genome and strongly implicate GC-rich repeat elements as playing a direct role in the pericentromeric localization of these events Genome evolution is dependent on the processes of eral independent reports indicate that genic segments, single-base-pair mutation and gene duplication. -
Rider Transposon Insertion and Phenotypic Change in Tomato
Chapter 15 Rider Transposon Insertion and Phenotypic Change in Tomato Ning Jiang, Sofia Visa, Shan Wu, and Esther van der Knaap Abstract The Rider retrotransposon is ubiquitous in the tomato genome and is likely an autonomous element that still transposes to date. The majority of approxi- mately 2,000 copies of Rider are located near genes. Phenotypes associated with Rider insertion are diverse and often the result of knock out of the underlying genes. One unusual Rider-mediated phenotype resulted from a gene duplication event. By means of read-through transcription, Rider copied part of the surrounding sequence to another location in the genome, leading to high expression of one of the transposed genes, SUN, resulting in an elongated fruit shape. Transcription studies demonstrated that Rider is expressed to levels comparable to the expression of other tomato genes and that control of transposition may be regulated by antisense transcription. Taken together, Rider is a unique retrotransposon that may have played important roles in the evolution of tomato and its closest relatives. Keywords LTR Copia • Phenotype • Rider • Tomato • Transcription Abbreviations ATP Adenosine triphosphate bHLH Basic helix–loop–helix BL Blind C Cut leaf or potato leaf mutation N. Jiang Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA S. Visa Department of Mathematics and Computer Science, College of Wooster, Wooster, OH 44691, USA S. Wu • E. van der Knaap (*) Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 44691, USA e-mail: [email protected] M.-A. Grandbastien and J.M. Casacuberta (eds.), Plant Transposable Elements, 297 Topics in Current Genetics 24, DOI 10.1007/978-3-642-31842-9_15, # Springer-Verlag Berlin Heidelberg 2012 298 N.